The eighth seeds lost 4-6 3-6 to second seeded team of Jean-Julien Roger and Horia Teacu.
Bopanna was appearing in his second season-end Finale, having reached the final with compatriot Mahesh Bhupathi in 2012.
Sania Mirza had won the WTA season-end Finale with Martina Hingis in Singapore recently and fans were hoping to see two Indians with Finals title in the same season but Bopanna's defeat poured water on those expectations.
Signs were ominous from the start as Bopanna was broken in the very first game of the match. They had a chance to get the break back on Tecau's serve in the sixth game but squandered two breakpoints to trail 2-4.
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In the second set too, it was the team of Julien-Roger and Teacu who got the first break and it stayed with them as they closed the match comfortably
In their favour.
Bopanna and Mergea, who teamed up for the first time in April, were contesting their fifth final together. They lifted Madrid Masters trophy and on the grass of Stuttgart and finished runners-up in Casablanca and Halle.